The report contains several parts, please see the following plot to get more detail about the report
Summary
Unique Genes: 248 Unique Isoforms: 1609
Gene classification
Characterization of transcripts based on splice junctions
Splice Junction Classification
Gene Characterization
Number of Isoforms per Gene
Isoforms Number x-Axis
Kown vs Novel Genes
Transcript Length
Classification
Normalized Classification
All Transcripts
By Structural Category
Mono- vs Multi-Exons
By Sample
Mono- vs Multi-Exons, By Sample
Exon Structure
Quantification
Gene Expression, Annotated vs Novel
Number of FL reads per Gene by type of gene annotation
Structural Isoform Characterization by Splice Junctions
Structural Categories
Isoform distribution across structural categories
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Transcript Lengths by Structural Classification
Exon Counts by Structural Classification
Transcript Expression by Structural Category
FL Count (normalized) by Structural Category
Subcategories
Isoform Distribution Across Subcategories
Transcript Expression by Subcategories
FL Count (normalized) by Subcategories
Transcript Lengths by Subcategories
Exon Counts by Subcategories
Matched Reference Transcripts
Length Distribution of Matched Reference Transcripts
Exon Count Distribution of Matched Reference Transcripts
Other Plots
Gene Expression between NNC and not NNC containing Genes
Splice Junction Characterization
Distribution
Distribution of Splice Junctions by Structural Classification
Distribution of Transcripts by Splice Junctions
RT-switching
RT-switching, all junctions
RT-switching, unique junctions
Comparison with Annotated TSS and TTS
FSM only
Distance to Annotated Polyadenylation Site, FSM only
Distance to Annotated Transcription Start Site, FSM only
ISM only
Distance to Annotated Polyadenylation Site, ISM only
Distance to Annotated Transcription Start Site, ISM only
Comparison With Annotated TSS and TTS by Subcategories
ISM subcategories
Distance to Annotated Polyadenylation Site for ISM
Distance to Annotated Transcription Start Site for ISM
ISM subcategories (%)
Distance to Annotated Polyadenylation Site for ISM
Distance to Annotated Transcription Start Site for ISM
PolyA Distance Analysis
PolyA motif
PolyA Subcategories
CAGE distances analysis
Multi-exonic FSM
Distance to CAGE peak of multi-exonic FSM
Multi-exonic ISM
Distance to CAGE peak of multi-exonic ISM
Multi-exonic NIC/NNC
Distance to CAGE peak of multi-exonic NIC
Distance to CAGE peak of multi-exonic NNC
Redundancy Analysis
Only FSM
Only FSM
Only FSM with CAGE support
Only FSM with polyA motif found
Only FSM with CAGE support and polyA motif
Only ISM
Only ISM
Only ISM with CAGE support
Only ISM with polyA motif found
Only ISM with CAGE support and polyA motif
FSM+ISM
FSM+ISM
FSM+ISM with CAGE support
FSM+ISM with polyA motif found
FSM+ISM with CAGE support and polyA motif
Intra-Priming Quality Check
By Structural Category
Mono- vs Multi-Exon
Coding vs Non-Coding
Bad Quality Controls
RT-switching
Incidence of RT-switching
Jounctions
Incidence of Non-Canonical Junctions
Incidence of SJ without SR coverage Junctions
By Structural Category
Incidence of NMD by structural category
QC Features of Bad Quality attributes across structural categories
NMD
Combined
Good Quality Controls
Cage Support
Annotation Support
PolyA Support
Junctions
Percentage of All Canonical Junctions
Percentage of Splice Junctions With Short Read Coverage
